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Sci Rep. 2018 May 30;8(1):8382. doi: 10.1038/s41598-018-26640-w.

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform.

Author information

1
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. claire.kim@channing.harvard.edu.
2
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. claire.kim@channing.harvard.edu.
3
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
4
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
5
Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
6
Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
7
Genomics, Proteomics, Bioinformatics, and Systems Biology Center and Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
8
Cancer Proteomics Core, Dana Farber/Harvard Cancer Center, Boston, MA, USA.
9
VA Boston Healthcare System, Boston, MA, USA.
10
Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

Abstract

The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses' Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours after collection, as well as those of samples collected from the same individuals 1 year apart. CVs were <20% for 99% of proteins overall and <10% for 92% of proteins in heparin samples compared to 66% for EDTA samples. We observed ICC or Spearman r (comparing immediate vs. 24-hour delayed processing) ≥0.75 for 61% of proteins, with some variation by anticoagulant (56% for heparin and 70% for EDTA) and protein class (ranging from 49% among kinases to 83% among hormones). Within-person stability over 1 year was good (ICC or Spearman r ≥ 0.4) for 91% of proteins. These results demonstrate the feasibility of SOMAscan for analyses of archived plasma samples.

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